Knowing the Difference
by Heather Giesbrecht
Summary: When everything has crashed down around you and nothing is the same. Does knowing the difference even matter ? Last in the Difference Trilogy. Chapter 12 - Smith Posted. Complete.
1. Prologue - Letter

**Prologue - Letter**

Dear Reader,

My name is Neo, I'm just a Rebel now, I was the One - until I found out the prophecy was a lie. So many things in my life have been lies lately. This letter detailing how I got to the Machine City could be the last thing I ever write. I don't write it to sound dramatic, its simply the truth. The leader of the Machines has asked me to record it 'for future reference'. Those words 'future reference' have given me some hope that I can survive.

What do I have to survive you probably wonder ? Answered simply, it would be the fight for my friend Niobe that I'm very likely to have with my now insane former love, the Ex-Agent A.I named Smith.

If it comes to that complexly, it's so much more than just saving one of my best friends, considering I just lost Apoc. It will decide if the Real world, the city of Zion and Machine-made dream world of the Matrix will survive. Smith has already taken over the Matrix and could try taking over the Machine City now if he wanted. Yet, I know that he won't. I can sense that he's waiting for me, no matter how long writing this takes. Smith has all the time in the world to wait for me. Who knows how he'll react to me, since it's been all over the place lately, because of that I don't know what's going to happen to Niobe, Smith or even me. Especially, not me and I can only hope that all this won't be in vain. I have to hope that Smith will... that I won't...

What could happen next terrifies me, even though I've died before. For you to actually understand that, I should stop stalling. I will record the last two days until now - all the encounters, thoughts, nightmares and dreams I remember. The only way I can do that without loosing my nerve is in third-person, bear with me.


	2. Chapter 1 - Planning

**Planning**

Two days ago...

Neo looked around at the dull metal walls and table of the Nebuchadnezzar's dining-room, at the three Captains'. Tall, short-black haired and dark-skinned Niobe of the Logos. She had arrived earlier this morning with her First-Mate Ghost and Operator Sparks. Shorter and pale-skinned Ballard of the Caduceus, who had been with them for the past few days. Along with his own dark-skinned and bald Captain, Morpheus of the Neb. He didn't want to risk the other Captains, Morpheus and his fellow crew-members said they'd help.

He pushed long black-hair out of his eyes, then asked " Niobe, Ballard. Are you sure you want to help us tonight ? You can still back out. Especially, you Ballard after the Bane-Smith ... incident. "

_'If Trinity and Morpheus can take out the Nuclear Plant's Reactor... Niobe wouldn't have to risk herself and Ghost. Plus I would have time to get into the Matrix's Source with Switch and the Keymaker. We're __**so**__ close to ending the war, Zion could be safe in just a few hours.'_

The Caduceus's Captain replied " Neo, you need all the help you can get. I talked to Malachi earlier, he's fine with helping. We'll take out the Plant's Control Room."

Niobe said " Ghost and I'll go after the Reactor itself. I hope we'll give you, Switch and the Keymaker enough time to get in the door."

Neo sighed and thought _'That's what worries me, if we don't have enough. If we fail it'll all be for nothing.' _He looked over as Morpheus spoke up " Trinity and I will be the back-up. We've got twelve hours before mid-night and the start of the plan. Does anyone have words that can't wait ? "

No one answered, Morpheus stood up rolled his stiff shoulder and the meeting finished. Neo winced as Morpheus did that wound was his fault, if Morpheus hadn't tried to save him the Captain wouldn't have gotten shot.

* * *

><p>He couldn't get out of the room and down the hallway's ladder fast enough. Stress had gotten to him lately. First with the Bane-is really Smith-betrayal. Bane'd had almost identical blue eyes and manners as Smith. It had hurt, still did since it'd only been revealed to him yesterday. <em>' Dear God, I don't want to think about Smith. He manipulated me, claimed he loved me. Was probably lying when he did. I hope he won't ruin the plan.' <em>

The second was the Keymaker's plan to get into the Source, so many things could go wrong. If someone would be a second too late or a second too soon. They had to get in without getting killed first. He stopped as he saw the Neb's First-Mate Trinity, standing in front of his door. The blue-eyed woman looked up and asked " Is the meeting over Neo ? "

He felt a bit awkward as he replied " Yes, Trinity it is. Everything's been decided, Niobe and Ballard are going to help us tonight." He didn't know Trinity all that well. He was closer to Apoc and Switch, than he was Trinity and Morpheus.

Trinity smiled slightly " That's good, hopefully it'll be over tonight. You should rest for a bit, everyone else will be too." She walked past him to her room, he walked into his own. Neo groaned as he laid down on his worn-out bed and thought _'Please, let Trinity be right. Let it be over soon.'_


	3. Chapter 2 - Lupa

_Author's Note:_

This means its a Memory and the End of a memory.

* * *

><p><strong><span>Lupa<span>**

Some time later the long, black-haired man looked up as someone knocked on his door. Neo blinked and called "Come in." before brown-haired Lupa walked in. He hadn't seen the man in weeks. "Lupa ? What are you doing here ? I thought you were in Zion. "

Lupa smiled and sounded relieved " Hello again Neo, I'm so glad you're all right. Had me worried the search wouldn't end."

A confused reply from him "You were worried about me ? I thought Ballard was the only one looking for us. I mean, Niobe she only found us after recon."

" Yes, I was. I'm also on the Vigilant, we were the other crew sent looking. Speaking of Ballard, I saw him and Malachi but I haven't seen Bane around. Did something happen to him ? "

Neo bit his lip and twisted a strand of his hair as he thought _' So, Zion sent Ballard and Soren ?. Why ? Sure, I'm the 'only one' who can end the war, but they should worry about Zion. Not me, now what do I tell him about Bane ? I don't want to explain what Smith told me, but I don't want to lie. Tell the truth that he's dead. Just not that it wasn't the original Bane that died.' _

Then his own hesitant "Yeah, something did. Bane was... killed about a week ago. Morpheus told Ballard to go back to Zion, so they could have Bane's funeral. Ballard decided it would be better if they stayed to help us. In case the Squiddies came back."

The first time he ever saw a Sentinel flashed in his mind.

* * *

><p><span>Memory, a year ago:<span> He had been listening to Apoc talk about Zion. How it was humanity's last city, their very last hope when an alarm had gone off. Apoc said " Come on, Neo. Hopefully this'll be the last time you see one for a while."

He questioned " See one of what Apoc ? " as the older Rebel got up and walked out of the dining-room.

Neo thought _' See one of what ? I don't like this, but if he's calm. It can't be that bad, right ? ' _as he followed Apoc down the right-side of the hallway. Past the Mission Control Room, to a ladder he hadn't noticed before. Going up the ladder to the third level he saw that Morpheus and Trinity were sat in the cock-pit. The metal was still shining, unlike the rest of the Hover-craft and there was a... a blue hologram of something.

Then his gaze drifted up the wind-shield, to what was hovering just outside it. He stared frozen at the Machines. They looked like a floating hybrid of a metal squid and clawed spider. Covered in silver metal they had spider-like ruby eyes and thin pincers around their mouths. Along with eight squid-like tentacles that ended in claws or most did, he couldn't really tell. _' What the Hell are those ? Do I want to know ? No, no I don't. Let them go away, whatever they are.' _

Apoc pulled him down in a crouch and whispered " Those are Squiddies, Sentinels. Eitherway their killing machines, if they find Rebel 'crafts and sense movement or ... "

Trinity hissed " Apoc. Be quiet."

Neo held his breath as one of the Sentinels hovered closer to the Neb. It's red-eyes seemed to glare at them. The Sentinel tapped on the wind-shield with a claw. It made a high 'tiing'-ing sound as it hit the glass. He felt like he was going to pass out as another one floated up to the first. This one had sensor-dishs on two of its longest tentacles. _'Damn it, go away, go away. Please, I don't want to die.' _

A soft sigh of relief as the Machines floated away down the huge tunnel.

End of memory, present time

* * *

><p><em>' Those are the main threat to Zion's population if they get in. They're not we're going to defeat them first.' <em>

Neo startled as the other man asked " Why's everyone sticking around here then ? Shouldn't you be waiting in the defensive line with us later ? "

" The reason we're staying here is simple. It's because we've got a plan to stop the Machines. If it works we won't need that line to defend Zion."

There was a strange glint in Lupa's gray-eyes as the man nodded.

* * *

><p>Neo couldn't help wondering what he thought. <em>'Is it relief that it'll finally be over ? Or does he like fighting the Machines ?'<em>


	4. Chapter 3 - Dark

**Dark**

Neo turned to look around at the dark forest, something felt off. Then he realized that the forest was completely silent, except for his own breath. He walked slowly as it started to rain. It dripped from the leaves into his hair and he shivered, remembered yesterday. Stared in shock at what he saw ... Smith and Switch. Heard his own alarmed cry of "Switch." She was tied up laying on the ground and Smith stood over her.

Her face was covered in blood, the blond woman blinked up at him and croaked "Neo, don't." He started to walk toward them, when Smith kicked her. Switch stifled a cry and he heard bone crack from the force.

Smith's icy-blue eyes flashed and he snarled "You worry about her. Her, Mr. Anderson."

He flinched at the old name, it'd been months since he'd heard that. _' It feels so odd hearing that, its not mine anymore. It never was.'_

* * *

><p>Neo woke up to someone knocking on his door and felt relieved when Switch called "Neo, come on we've gotta get ready and get the Keymaker."<p>

_'That was a weird night-mare. At least, at least Switch's fine. '_

Pushed himself up and replied as he got up "Okay, how much time do we have ? "

"Soon, everybody'll be ready, then we do our thing and wait until the Plant's shifts change. Until then we've got to get the Keymaker. "

_'Great, just what I've been waiting for. '_ he thought as he opened the door and walked out.

When Switch smiled it was grim " Yeah and its close the hotel."

He followed Switch up the ladder to the M.C.R. To see that Apoc, Morpheus and Trinity were waiting in the Matrix, Tank sat in the Operator's chair. He blinked as Tank smiled at him and asked "Ready, Neo ? "

He nodded and walked to his chair, pushed his hair back before he sat down and took a deep breath. Tank came over and said excitedly "Man, if tonight works. If it works we're partying tomorrow and you're my favourite person ever. "

_'I really didn't need that hanging over me too. Thanks Tank.'_

Neo winced more from Tank's sudden attitude shift then pain as he appeared in the Matrix.

* * *

><p>He opened his eyes, as Switch appeared beside him, he tied his hair back. <em>' I really don't want it getting in the way tonight. We've got too many places to be at for me to leave it loose.' <em>Then they walked toward the door, Morpheus said "Good-luck with getting the Keymaker, we'll be waiting at the Layffette with the others."

As he and Switch walked out, it reminded him. They only had an hour before everyone would arrive for the meeting. When they got to the car, he got in the driver-seat and Switch sat beside him. She shook her head and asked "Why wouldn't he send Trinity with you ? This is too important for me."

He started driving before he replied "No, it's not Switch. Anyway, it's better you're with me. We're comfortable, Trinity and I not so much."

Switch laughed "Yeah, it's nice to know I've got more friends than just Apoc, you and Dozer."

_'I don't really wanna bring it up, but we've got twenty more minutes until we get there. Just do it.'_

"Switch ? " The white-haired woman nodded and he continued " Do you have any idea why Dozer and Tank avoid me ? Or Tank did until barely."

"Well, it's easy really, Neo. Until you came along we didn't have much hope of surviving. Plus, Morpheus was sure about you and wouldn't shut up. They got annoyed and figured you'd be friends with Morpheus and Trinity rather than Apoc and I. They were worried you'd turn arrogant like Cypher after he got freed. Well, Cypher had problems before he went bat-shit."

* * *

><p><em>'Did Morpheus do the same with him ? Expect when he found out Morpheus lied, he went and betrayed us ?. Dear God, that reminds me of Smith.'<em>

The dark voice snuck into his mind with _' "You missed me ? " _

Mentally, Neo hissed _'Smith, shut up and go away.' _

Mockingly, Smith stated _"You're an idiot to think you can stop this. A hundred years it has gone on and you think __**you **__can end it." _

He replied '_I will do it somehow, I will. Zion won't have to be afraid when its over. ' _As he shook Smith's voice out of his head, he noticed they were close to the Keymaker's hiding place.

* * *

><p>Startled as Switch's voice broke in "Are you all right Neo ? You just pulled some odd faces for a while. "<p>

"Sorry, I got distracted. Should we stop here ? "

"Sure."

He left the engine on and they got out, walked up to a shabby, dark-gray two-storey house. He didn't like it something was wrong. Then Neo looked up the street, to see that a silver car was parked ahead of them, " I think Frenchie's twins are here or someone else is. "

Switch replied as they walked in "Let's say "Hi." shall we ? "

* * *

><p>Neo grinned slightly, before he calmed down. Ready to fight for the Key-maker.<p> 


	5. Chapter 4 - Keys

**Keys**

Neo looked around the inside of the house, light-walls and a dark-wooded stair-case. The Keymaker's voice shouted "Help !." from the second level. His vision flickered into code and he saw the old man with a blond Were-wolf and pinned by a red-haired Vamp.

He ran up the stairs as the Were growled " You're going back, old man. There's no stupid pretty-boy to save you now."

He hissed "Whoever you are. I am not pretty." _'Damn it I'm not.' _while he jump-kicked the Were in the back. Blondie went flying and crashed through the wall.

Neo heard "My keys, I lost my keys." from the Keymaker, while the Vamp lunged at him. He jumped above the Vamp and twisted out of Blondie's reach. As he landed the Vamp slammed into his back, he rolled over. Got up and kicked the red-head and shouted "How'd we get rid of 'em ? ".

No answer from the old program. He'd thought _'At least, they aren't damned mutant ants this time. Wait, Niobe said Vamp code can be stopped with a stake.' _The Keymaker had disappeared from his sight. Neo leaned down, grabbed, twisted and threw the Vamp into the stair-railing. Meanwhile, Blondie had changed into a bi-pedal, yellow-furred wolf and gone after Switch.

* * *

><p>He ran, jumped and flipped off the landing before he turned in mid-air and landed on his feet. The Keymaker had gotten pinned in the living-room by a tall, brown-haired program. For a second it wasn't a random program, it was Smith. He stared and forgot to breath, <em>'It's not him, even if it was he doesn't care. '.<em> Frozen for that second Neo got floored by the Vamp. Thankfully, the illusion of Smith had disappeared as well.

_'Balroan Hells, damn it we don't have time for all this fighting.'_

The Vamp glared and hissed at him, until he surprised it by throwing it into a table_._ Then the Keymaker called "I've got my keys. Find me a locked door and we're out of here." Neo turned his head, to see the brown-haired program was sense-less on the floor. _' How did that happen ? I thought he didn't know how to fight. ' _

Switch exclaimed "There's none up here !. They all have dead-bolts. Neo, can you find any ? "

He got up, rushed past the Keymaker, across the living-room and into the kitchen.

* * *

><p>Then looked around for a back-door. He called back "There's nothing. How can there not be any ?"<p>

The Keymaker "What about the front ? Just lock it. " At those words Neo felt like running **into **a wall, not up it.

Switch called a few moments later "I got it." He felt relieved, rushed out and round-house kicked the Vamp. Who'd been sneaking up on the old program.

Said program turned to look at him " You didn't have to do that... oh, well. Let's get out of here."

_'He's crazy, the old program's crazy that Vamp would've killed him.'_

He shook his head and followed the old man to the door. Stared as it was unlocked to reveal not the street, but the inside of the Lafayette hotel. They walked in and Switch asked "What about the car ? "

"I forgot all about it. There's no time now." Neo shrugged and walked up to the meeting-room.

* * *

><p>He hoped the meeting would be quick.<p> 


	6. Chapter 5 - Wait

_Author's_ Note: Lots of speech in this chapter and maybe the next.

* * *

><p><strong><span>Wait<span>**

Neo, Switch and the Keymaker walked into the meeting-room. He felt the nervous excitement coming from the waiting Rebels. He looked around at the old, green-walled room. There were a few padded chairs scattered around. One was white, the other green, and the last was a familiar red one. The same one from a year ago when he'd been freed.

Niobe sat in the white one with Ghost standing beside her on the right. Ballard sat in the green with Malachi on the left, and Morpheus in the red with Trinity on the right. Apoc was standing on the left side of Morpheus, he and Switch moved to stand with their friend. He watched as the Keymaker walked to stand by Niobe and Ghost.

* * *

><p>Then Niobe said, brightly "Switch, Neo. Nice to see you two again."<p>

He smiled at his other friend "You too Niobe, Ghost." as he nodded to Ballard and Morpheus.

Niobe continued a second later "So, you're the Keymaker, I've heard so much about. The one who came up with this plan."

The Keymaker responded "Yes, I am. You need to remember you only have five minutes to set the bomb in the Reactor and get out."

Niobe smiled and replied "I know, but I like challenges. It wouldn't be one if I didn't have a time to beat."

Neo jumped as Morpheus cleared his throat and turned to look at the dark man. His Captain's gaze moved, slowly, around the room. Neo shivered as it stopped on him.

* * *

><p>Morpheus asked, suddenly "Do you all believe that the war will end tonight ?"<p>

_'Believe it, yes. Yes, it's the only thing keeping me sane... besides the adrenaline.'_

He and the others responded "Yes."

"Our hope stands on the edge of oblivion, do you **truly** believe it ?."

They all exclaimed "Yes!."

Morpheus continued "You all know we only have a limited time to pull off this plan. The worst part you face now that the time has finally come. That is knowing you and every single one of your friends could die tonight. So, tell me now is your own life and your friends lives, are they worth giving up for the sake of humanity's freedom ?. "

_'My life for Zion, for all of humanity of course it is. We've done everything to save them, waited bleeding and hoping to bring them peace someday. We'd do anything, even give up our friends to end it. Everything I've done in this war was for my friends or my love. No matter how stupid my choice of a love is, was. Damn it, I don't know what to think of him.'_

He answered "Everything we've ever done is for all of them. It's what we've lived for, what's let us get through it all." as Morpheus stood up and paced.

Then his Captain asked " Every drop of blood ? Every bit of pain you've experienced since you became free ? Absolutely everything, are you sure ?. "

Neo shifted, the adrenaline hadn't faded yet. He wanted to do something, waited to finally go. He was distracted briefly as he saw Apoc and Switch nod in agreement. He wondered briefly how many friends they had lost. Everyone else had started to look impatient too, even the Keymaker.

_'All the more reason to end this damned thing. Yes, absolutely that mean's there was a reason for my guilt about the real Bane's death by Smith. I wish I'd actually talked to him for more than a few seconds. I would have known it was Smith not Bane. Either way, everything'll be worth it tonight.' _

He noticed as Ghost shifted by Niobe's chair and the Logos' First-Mate replied " Every time we've gotten injured or nearly died while saving someone. No matter who it was, we were building our inner strength up."

Malachi interjected "Yeah, we wouldn't think of doing this otherwise. We'd be running away instead. All our friends are counting on us, it's like we were... " Malachi trailed off.

Morpheus smiled and launched into an excited speech "Like this is our fate or our destiny to be here ?. My friends, I believe everything has lead us to this. Our shared experiences have brought us together now. The bad even more than the good. Why is that ? Simply put without the strength of our friends and their support ... in the worst of situations we would have died. We are stronger than the Machines. The Machines work together because they have to, not because they want to. Unlike them we are united by choice. This is the night we've waited for. Tonight we will end this war once and for all. "

* * *

><p>Neo grinned and cheered with the others. Around him the others started to talk. Morpheus looked at him and Switch, then nodded. <em>'We can finally get going. Thank God, I couldn't stand waiting any longer.' <em>

He pulled his shades out, surprised they were still in one piece. He laughed again and put them on. Switch pulled her own shades on. Then he, Switch and the Keymaker walked toward the door.

He heard everyone wish them "Good-luck." as they stopped in front of it. The Keymaker locked then unlocked and opened it. Neo thought _' We've got thirty minutes to take out the guards. Once and for all, no more waiting. No time for more worrying, until we get in the Source hallway at least.' _as he took a deep breath to try and wait out the adrenaline. It didn't work.

Then the two Rebels and program walked into the Source building.


	7. Chapter 6 - SWAT

_Author's Note :_ Thanks to _blackcat21223_ for the favourites.

* * *

><p><span><strong>SWAT<strong>

Neo walked out into the open with Switch. They had to get from the twenty-second floor to the forty-second without missing any of the guards. They absolutely couldn't get interrupted by Agents. His vision changed into code and he saw four guards farther up ahead. Nodded to the woman in white, then ran along the wall to jump off and kicked the closest one in the face. Flipped over as Switch punched the one nearest to her, he landed and grabbed, then threw the farthest one into the wall. Switch kicked the last one as the Key-maker walked into the hall-way.

Ran ahead to the next level, hissed as he saw a few SWAT members standing down the hall from him. He recognized the Captain, the guy who had shot him in the shoulder when...before, before he'd been killed. His shoulder twitched as he remembered the pain. _'He's going down he wanted to kill everyone. Not that I would've minded if he'd killed Cypher the bastard. Still he can't get away again, I wish Morpheus would've let us have guns. Of course he's right, they'd have made too much noise.'_

Needed to take out their shields before Switch would have a good opportunity to get in. Crept down the hall believing he wouldn't be seen, until he was behind one of them. Grabbed the nearest SWAT and threw him into the others, they fell to the floor. Punched the Captain who was getting up as Switch swept into the fight. Angry recognition in the man's gray-eyes as the Captain blocked his kick. Surprised to find himself falling as the SWAT tackled him. They rolled over a few times before his shoulder smacked into the wall. Hissed as he got punched in the face, Switch was suddenly choking the man into unconsciousness.

"C'mon, Neo. We don't have time for draw-outs remember."

All the fights blurred into one huge confusing mess.

* * *

><p>As soon as they stepped onto the forty-third floor the fights stopped all together. <em>'Don't tell me they'll have Agents' waiting for us.' <em>

Switch and himself scanned all the rooms on the floors before they'd let the Key-maker on it. Neo'd barely caught his breath as the city's lights started to go out and turned for the door. It looked just like all the other doors but apparently it had to be this door. The Key-maker asked as he unlocked the door "Are you ready ?"

Switch replied "As we'll ever be, let's go."

Another surge of adrenalin as he entered the white, green-doored hallway. _'Only twenty more minutes and the war should be over. Still this is way too easy. It was just SWAT, not a single Agent. I don't like this at all.'_

His adrenalin soon turned to impatience as the hall-ways all looked the same. Both of the Rebels asked simultaneously "How much farther ?"

An answer of "Just a little bit." as they turned around a corner like all the others.

Neo's throat felt tight as his heart tried to beat through it. Smith smiled at him "Hello, love."


	8. Chapter 7 - Crazy

**Crazy**

Neo stuttered over the words "W-what a-are you doing here ?"

_'W-why ? How did he find me ? Even if I still lo-, no... even if yesterday hadn't happened. That's more than creepy.'_

Smith's eyes glowed as the Ex-Agent walked up "Well, I could not let you do all the work. It would have killed you to do it by yourself."

He glared hurt and angry "Just what does that mean, Smith !?."

The green-doors around himself, Switch and the Key-maker opened. One of Smith's copies ran a hand over his cheek "You could say that I have been helping from the side-lines."

_'He killed them, he just killed more people. I knew it was too easy. Why wasn't Bane enough ? Why couldn't he have just told me before ?' _

Snapped back "I-We could've handled them. After what you did yesterday... I-I don't need your help, you lying son of a bitch."

Blinked as he was slammed into the floor by a back-handed blow. Licked blood off his lips as Smith glared down at him "You could at least appreciate what I did for you, love."

He groaned "Oww, never said I didn't. First my shoulder, now my face. Haven't I gotten beat up enough today ?"

Smith leaned down to him as Switch tensed.

While the Key-maker exclaimed "We don't have time for this. It needs to be stopped."

* * *

><p>Fingers slid around the back of his neck, tilted his head slightly up. Smith kissed him softly, then pulled away to glare at the Key-maker. Blue-eyes were angry as Smith hissed "You lied to him," those eyes looked back at him and softened. A hand ran through his hair as the brown-haired program continued " If you go into that room Neo, you are just going to be delaying the inevitable. They all lied to you it is not going to stop."<p>

Switch moved to pull Smith away from him. Instead one of the copies grabbed and pinned her against a door. Switch choked out "What are you talking about, Smith ?"

A tanned hand pulled him up and gently pushed him toward the door. "See for yourself, Neo."

_'I liked it better when my love/ ex-love/ whatever-he-is wasn't insane. He really was good at hiding it. I've never seen anyone switch moods that fast.' _

Neo turned at the door as he heard Smith's copies move out of the way. Switch and the Key-maker joined him a few seconds later. As the old program unlocked the door Smith smiled at him again. He shivered as the door creaked open. _'I don't know what to believe anymore.' _


	9. Chapter 8 - Archi

**Archi**

Neo sighed as Switch and the Keymaker walked through one of the other doors. Stared down at the key for a second before he put it in the lock and turned it. Instead of opening, the door cracks filled with light and even with his shades it was impossible to see. When the light faded he stared he suddenly stood in a white-room.

_'How'd I get here and where is here anyway ? Why are there so many screens ? Who's that creepy old guy ?'_

An old, white haired, bearded and suited man sat in a white chair. The screens around the room suddenly switched on. They showed himself with the old man, over and over. It was really disorienting and he closed his eyes, before he asked "Who are you ? Where am I ?"

"I am the Architect and this is the Source."

Opened his eyes, then tilted his head "As in you helped make the Matrix ? "

"Yes, I did and all the versions before it. Along with the two Beta versions of course."

_'Versions ? How long would it take to make a new version ? This...either Smith is right or something is terribly wrong. How long has this damned war been going on ?' _

He paced around the edge of the room as he tried to fight the panic those thoughts instilled. Found himself taking a deep breath before he stated "Smith was right."

Archi sighed as if already impatient with him "Of course Smith was right, he is not in the habit of lying like a human. Though, you did not truly think you were the only One. Every version of the true Matrix has had one, this is the sixth version. The problems we've had with this version are rather unique, not only is this his fault but it is also yours and Morpheus's."

"**You can't blame that on us !**"

"Yes, I can. Shall I show you how, Neo ?"

He stopped pacing to glare at the old program and snapped "Fine."

* * *

><p>Screens flickered around him to show Trinity putting a bomb under the Agents car and walking away. Then it switched to Smith leaning over him in said car and looking concerned. Before it flickered into himself, Apoc, Switch and Smith as he stumbled into the first-floor room to die because of Jones. Finally it showed him standing inches away from Smith in the white train-station. The first time he'd said "I love you." to Smith it caused him to flinch from conflicted emotions - love, doubt and betrayal.<p>

Neo ran a hand through his hair, the screens suddenly showed that too. He stated "That doesn't explain how your 'problems' are any of our faults."

Archi shook his head in contempt and amusement "Oh, they do you just don't want to see them. Let me fully explain - if Morpheus had not ordered Trinity to place that bomb under the car, Smith would not have had a reason to sympathize with you. If he had not sympathized with you, you likely wouldn't have fallen in love with him. You shouldn't have anyway considering we coded her specifically for you. Yet, because of that the sixth war became different in ways that I did not intend. Thusly it has gotten dragged out far longer than it should have. In any other version Zion would have been destroyed and started over months ago."

_'Archi is crazier than Smith, he wanted to __**force**__ me to fall in love with Trinity. It's a good thing she and I didn't get along very well then. Wait, what's that mean Zion would've been destroyed ?'_

"That's the difference you can't force people to fall in love, much-less code it into someone. Still knowing the difference between what's real love and what's not is confusing sometimes. Not that you'd know the difference if it came crashing down on your head. Now, why would Zion have been destroyed ? I thought... but then since there have been other Ones. It's not about 'saving' Zion at all is it ? So, what's it really about then ?"

The old program almost seemed to smile as he replied " Reloading and restarting the Matrix every one hundred years. The Oracle who helped come up with the plan is supposed to send the current One to me. You see the One has the Prime Program hidden inside their own code, for some reason it will not mesh with an A.I's code. So, the human Ones are necessary to the Matrix's existence until they reach here. By the time the current One reaches here the Matrix has started to destabilize itself. Now it is made worse by Smith's having started to destroy it."

Screens filled with images of Smith and his copies taking over people.

* * *

><p><em>'The Oracle helped this bastard ? She knew all along she was sending me here to...to die for this things existence. No, I refuse. she's betrayed me just like Smith did. Even worse than Smith did, not only did she lie to me, but to all those other Ones and who-knows how many other people. Is she manipulating Smith too somehow ? Huh, it wouldn't surprise me now.'<em>


	10. Chapter 9 - Answers

**Answers**

Neo shook his head as he stared at the screens of Smith. At the white walls, as he turned again he noticed the two doors. One on the left, the other on the right. _'One of those is my way out. I've got to get out and tell Smith. If the Oracle really is manipulating him too, he needs to know.' _

The Architect sighed and he turned to the program in white. "It won't matter if Zion is destroyed. We just need you, but as I see you will not. Then this should interest you."

New images filled the screens, images of Smith and Niobe. Niobe was being dragged out of a purple Mustang. Anxiety filled him while the dark-skinned woman started fighting Smith's copies. She was doing well really, as she knocked two into the car.

Found himself reaching out when one of the Smiths' snarled and grabbed Niobe's shoulders. As he watched the copy threw Niobe down, after Niobe's head slammed into the street he waited for her to get up. She didn't and the copy picked her up. In the background he saw Ghost surrounded and shooting at the Smiths'.

Exclaimed, "**Smith**, no, no, don't. You can't…you bastard." when the one holding Niobe disappeared out of sight. The rest of the copies abandoned Ghost who, uselessly, ran after them. After a shot of Ghost's devastated expression the screens went black.

He demanded, "When did that happen ?"

_'This can't be happening, crazy or not, it can't be. Why is he going after Niobe ? He's got no reason to kidnap my friends.'_

Archi was, as always, calm, "A mere minute ago. The left one is the way out."

Most words failed him, "Fuck, damn it." _'I don't want to… but I have to, I can't let Niobe die. No one else is fast enough, or strong enough to save her.' _

At that he turned toward the doors and walked to stand between them._' He really thinks I'll fall for that trick ? But, what if it is the safe door ? Damn it, I don't have time for this.'_

The voice from when he died said in his mind, _"The right. As this is your path you must finish it.' _

Desperate he replied to it, '_But, how ? Where do I go ?' _

_"To find your answers."_

_'What ? What's that mean ?'_

This time there was no answer and trusting the being he opened the right door. Archi called, "Whether you succeed in this or not, Neo, we will not meet again."

As he walked through he quipped, "Lucky for you cause I'd delete you next time." and slammed it shut behind him. Decided to go back to ignoring the pain as it flared._ 'I need to know where Smith took Niobe. I need answers and the Oracle knows something about this; I have to find her.' _

Started running for the door that the others had used. When he opened it, it led into the office's hallway, not the backdoors. If he had to run all the way there it would be too slow, he had to fly. His cell rang and he answered, "Neo."

Seraph's voice, "She wants to talk, we are at the old building again. Can you make it ?"

"How'd she know ? Never mind, sure, I'll be there. Tell her she better have answers."

"That is for her to decide." After those words the other end went dead.

Growled as he kicked out a window and backed up. Out of the corner of his eye he saw the familiar faces of the cops from the hotel staring at him as he threw himself outside. Looked back for a second to see that they'd rushed to the window after him.

A few minutes later he had landed on the Oracle's roof. Didn't really remember going into the actual apartment, just that one second he was on the roof and the next Sati was hugging him.

The little blond program beamed, "I'm glad you're okay."

Despite his current mood Sati's smile was infectious and he returned it. "Me too, Sati. What happened to your Dad and Mom ?"

"They had to leave again after they dropped me off. Father told me to wish you "Good-luck." So, good-luck."

A throat cleared and he looked up to see the Oracle standing in the doorway. Or someone who looked like her at least. The Oracle was somewhat shorter and thinner than he remembered. Besides that she wore the same green-dress as all the other times. When he got up she moved into the kitchen and he followed. It was still the same green-walled room with the dark-wood cup-boards. That sameness was disorienting with everything that had happened since he'd first set foot in here.

Looked back as she asked, "Seraph would you take Sati to look at the stars ? Just for a little bit, Neo and I have some things to talk about."

Shifted nervously as the white-clothed program nodded and led Sati out. When she offered a plate of cookies to him, he couldn't believe it and shook his head.

In response she put the plate down and said, "You first, Neo."

That pitying look in her eyes made him demand, "Is it true ? Are you the Matrix's Mother ? Did you know you were sending me to die ?"

Despite the Architect's words now that he saw her doubts plagued him. _'It can't be, Archi was lying, surely he's capable of it. After all he has to be lying, it can't __**really **__be true.'_

When he finished the questions he sank into the chair, stared at her as she lit a smoke and took a drag. She looked away and replied, "I'm sorry, Neo but it is true. I am the Mother of the Matrix. I knew from the beginning that if you didn't have a reason to live, it was likely you'd choose to die in the Source...like the others."

"What about the Prophecy ? Is it a lie like he said ?"

His heart sank at the answer, "Yes."

'_The Prophecy was a lie and I'm not the One, I'm just a Rebel. None of the so-called Ones were either, but I'm not them. It doesn't matter if I die, somehow I'm going to stop this like the others never did. I'm going to save Zion __**and**__ Niobe before it's too late.' _

Then anger mixed with his desperation, he slammed a fist into the table, "Why didn't you tell me it was a lie ? Everything we've ever done was to end this, not start it all over again. Why didn't you tell me the truth ?"

"I couldn't."

"Why not ? Who said you couldn't ?"

"He's sitting right in front of me."

_'How's that work ? It doesn't make sense.'_ Heard himself say the words out loud.

"It's all about the choice you made when first came in here. You decided you **needed** to know if you were the One and about Morpheus. At that time you also subconsciously decided you weren't ready for the info about the Prophecy and such until now."

Shook his head, "You're going to claim that's why you didn't tell me about Smith's being back isn't ? That I couldn't decide if I wanted to know ?"

Again she nodded, "Keep going."

"Well, now Smith's kidnapped Niobe and I don't know where she went. I need to know."

"I can't tell you where she is."

Pushed his chair back roughly as he stood up, "Then you can't help me anymore."

Turned away to start walking out and she called, "Neo, wait. There's one thing I can still help with."

"Really, what's that ?"

"It's Smith, the more people he copies the stronger he gets. He's far stronger than before, so much so that the Machines can't stop him anymore. However they can still trace him in this mess of code. If anyone knows where he has Niobe it'll be them. Neo, if you can't convince him to stop he won't. Not until everything in here and in the Real is gone."

Once again he turned back and nodded, uneasy but grateful, "Thanks."

_'God, I hope it won't come to that. Now I've thought it though, it probably will.'_

"Good-luck, kiddo, I think you'll need it."

'_Great, so, now I need to get to the Machine City. If I do get there, I'll have to go into the Matrix. Since Smith kidnapped Niobe he'll be waiting for me. Fantastic.'_


	11. Chapter 10 - Truth

**Truth**

Neo opened his eyes and saw that Switch, Morpheus and Lupa stood around his chair. _'__Isn__'__t Lupa supposed to be with Soren at the defence line ? Is Soren around here too somewhere ? God, I don__'__t wanna tell Morpheus. Who knows how he__'__s going to react.__'_

Apoc un-jacked him and he dizzily pushed himself up, everything felt like it was spinning as he shut his eyes. Switch asked, "All right, Neo ? You look paler than normal."

He managed to reply, "It's just my shoulder 'n the other stuff." Forced himself to open his eyes to focus on the metal beyond his Captain and friends, Lupa's green-eyes glowed in encouragement.

Morpheus asked, "What happened ? Why did you go to the Oracle ?"

That made him bite his lip and rub at his shoulder, his words were hesitant, "…The Prophecy…it's a lie. There is no One, according to Archi, well, the Architect there's not going to be any more Zion, but that doesn't matter because they've destroyed it before was what I got from the implications."

Morpheus shook his head, "No, you must have missed something or misheard it. It must be real."

"I'm sorry, Captain, but that's why I went to the Oracle. I didn't really want to believe it, but Morpheus she confirmed it. Plus, I went to ask her where Smith took Niobe, she said I'd have to go to the Machines because the code is so corrupted."

Morpheus's face was shocked as the info sank in, then the man asked, "What do you mean 'Smith took Niobe" ?"

Switch put a hand on his shoulder to steady him as he got up. Despite how unsteady he was, he had to convince Morpheus to let him go, "Exactly that, I watched it happen, Ghost couldn't do anything. The Prophecy might not be real, but I **need** to save her from Smith. She didn't do anything to him and it's my fault he went crazy in the first place. Jones only gave him that virus because he wanted to avenge me. This will never end unless I can get to the Machines and stop the war here and Smith in there."

Ghost's voice as he entered the Core with Sparks and Trinity, "I'll go with you Neo, you'll need someone to help get her out and un-jack her if Smith attacks you; which he probably will."

He could imagine Apoc shaking his head as the pony-tailed man said, "No, Ghost, you and Sparks are too valuable to the Logos. I've worked on her when you needed our help, I'll go with Neo."

Lupa chorused, "I'm in too, the line failed Soren, Ballard and the others are dead, but, at least, I can help somehow like this."

_'__Soren is dead ? Poor Lupa and he had to watch it. How many more people have to die ? I don__'__t want to know, but, doubtless there__'__ll be a few more. I__'__m sorry, Ballard, Soren, I__'__ll stop this. You guys can kick my ass if I don__'__t.__'_

Morpheus looked at him, Lupa and Apoc slowly as if he'd lost all the certainty he'd ever had. "If you three are sure it will help to end this for Ballard and the others' sakes, I won't stop you. I'm just not sure if this will work."

With those words, Switch let go of him, then he, Apoc and Lupa left the Core. Apoc stopped him to say, "You want something for your shoulder ? When we get there you're not gonna want to be distracted by pain after all."

Apoc's confidence made him smile. _'__At least Apoc, Switch, Ghost and maybe Lupa believe I can do it.__'_ Nodded before he replied, "Sure, it can't hurt." They walked into the Med bay and Apoc pulled out a painkiller needle as he sat down on the table.

Lupa looked around and ran a hand through his brown-hair nervously. Slowly, he reached out to put a hand on the gray-eyed man's shoulder. "Lupa…are you **really **sure that you want to do this ? Soren wouldn't blame you if you don't go with, Apoc and I won't make you either."

Lupa nodded and moved away from him to the wall, "I know, but I feel like I have to do this."

He pulled his sweater and shirt off, then winced as Apoc slid the needle directly into his shoulder. After he pulled his shirt and sweater, back on they left the Neb and walked the short distance to the much smaller Logos. The relief he felt that the pain had really started to subside was great, but found it replaced by tiredness.

When he nearly stumbled into a door, Lupa laughed, clapped his shoulder and said, "Maybe you should get some sleep, you'll need it more then we will. Apoc and I'll get her started."

Gratefully, he nodded and then went to the bathroom, before he stole someone's bed.

**Nightmare**

He stood in the office where everything had started. The green-walls and huge windows, the couch by the door, all the same as before. The long black-haired and gray-eyed man from in the elevator glared at him, "Traitor, I told you doomed us. Now you're going to pay." Said rebel stood over him with a knife covered in electricity.

A hand landed on his shoulder, he spun to see that Ballard was giving him an accusatory look. "If you hadn't put it off, I'd still be alive."

Ballard let go as excruciating pain lanced through the back of his neck. As he fell to the floor, he screamed.

**End Nightmare**

He opened his eyes again and saw that a very panicked Lupa leaned over him. Lupa shook him and exclaimed, "S-something's **w-wrong** with Apoc ! We, we went a little bit and then the engine or one of the fuses or something…it just, it died. He said he was gonna go and fix it. Ex-cept, **except **he hasn't come up and the engine hasn't started…I-I think he might've knocked himself out. Come on, **come on !**"

Worry filled him, hurriedly he got up and followed Lupa down to the Logos engine-room. Like every other room the floor was made of corrugated metal, the fuse-cases lined the walls. It was still warm here seeing that the engine hidden under the small-floor hatch. Said hatch still lay open in the center of the room, a light was hooked onto the ladder's-edge.

_'__Lupa didn__'__t even go and check it sounds like, maybe he fell asleep before he fixed the problem. There__'__s nothing to say that__'__s he is actually hurt. Besides after what Lupa just witnessed it makes sense that he__'__d assume the worst right away.__'_

He called, "Apoc ? Apoc, are you all right ?" No response from his best friend, then something slammed into the back of his head.

Apoc whispered from above him, "Neo ? Neo, wake up."

As he struggled to open his eyes, random spots flickered in front of them. Shock flooded him as he realized what had just happened. _'__Lupa just knocked me out. Lupa just knocked me out. Why would he do that ? Did he snap ? He must__'__ve.__'_

There was rope tied around his wrists, he lay on the floor inches away from the engine. Despite the darkness, he felt Apoc's presence beside him. His shoulder throbbed again and now his head ached too. For a second he tried to form words and all that came out was gibberish. Finally, he managed to say, "A-Apoc ? Ow. Is…did Lupa snap ?"

Lupa's laughter echoed from in front of them, "I never wanted to be like Smith, yet I ended up **exactly** like that idiot. Well, he might have gotten rid of my copies but that doesn't matter. Do you know why ? That's because it's so ridiculously easy pretending to be human. You're whole race is a bunch of self-serving **idiots** who can't see an inch in front of your collective face. All I had to do was pretend that a few missions had shocked me and they ate it up gleefully. That made it even easier to get close to the EMP and absolutely decimate that so-called 'defensive-line'."

Shook his head in denial, he had to be imagining this. He absolutely had to be having another nightmare. "You're crazy, Lupa, you're fucking crazy."

_'__He killed Soren and Ballard__…__and who knows how many people. He snapped, he snapped and nobody__'__s here to help us. If we can__'__t get free, everybody__'__s going to die. We might have to kill Lupa to save Zion.__'_

Apoc muttered, "That's not Lupa, Neo, that's Jones. He did the same as Smith, we all got lied to again."

Blinded as the heavy work light was turned on, then dropped to the floor. When the light and the spots in front of his eyes had settled he saw what Apoc was doing. The long black-haired rebel was sawing at his ropes with a shard of metal. His gaze turned back to the brown-haired man. No excuse would explain why Lupa's gray-eyes glowed with the same malice and crazy as Jones's dark-green ones.

Yet, he found himself starting to believe Apoc as Lupa/Jones growled, "After everything Smith took from me, he doesn't need **you** too. I don't even know why you like him - he's erratic, emotional as a rock and just as ugly. There's no reason for you to even think of liking him."

It made him laugh as Apoc sing-songed, "Somebody's **jeal-ous**. Poor little Jones was outmatched by Smith again. Obnoxious and jealous, how'd you stand this crap, Neo ?"

He smiled, "I don't know I can't stand now." As Apoc snapped his ropes and lunged at Jones. Apoc slammed the brown-haired being into the ladder, as he squirmed his way toward the metal shard. Things happened so fast that he couldn't remember how he got freed - just that one second he was trapped and the next he wasn't.

Over the past however long had passed, he'd heard a lot of scuffling, grunts and cursing. A metallic thud signalled that Jones and Apoc had crashed into one of the walls. When he looked toward them, he saw that Apoc was bleeding from his mouth and now pinned against the far wall. That spurred him to grab Jones haul him off Apoc to spin around and throw him to the floor. When Jones landed he kicked the man's side, Jones grabbed his leg and pulled. Off-balance, he crashed heavily to the floor and lay winded from the sharp surge of pain that signalled the painkiller was gone.

Jones had scrambled up and grabbed the light from the floor. It looked like Jones was going to go after Apoc again. Anger made him grab Jones's boot, said boot smashed into his face before the man fell. The last thing he saw normally was a brightness as Jones twisted and swung the light at his face. He screamed as it connected and everything turned to a sharp, searing agony.

_'_**_Oh God, God dmanit, fuck. Augh, gah-aa, burning, stop it. Make it stop. Please.'_ **

Dimly, he heard Apoc shout, "Neo !" All the while, he clawed at his eyes as he tried to get the glass shards out. That was just before he smelled burned flesh, tried to open his eyes and couldn't. There were two reasons: one - it hurt like fuck and two - it hurt like a god damned fucking Balroanian hell.

A welcome distraction from the pain as he randomly wondered, _'What's a Balroan or a Balroanian hell ? Even after all this time, I still don't know what that means, if anything. Maybe that afterlife voice knows what it means, I should ask it next time.'_

Something caught his interest, it was all around him - a fading gold light on black that he realized was cooling metal. Then he 'saw' something else it was different from the metal, it was an orange fire shaped like Jones's RSI. Seconds later the fiery form burst into a shower of crackling and dying sparks on the floor.

He startled as Apoc's hands suddenly touched his face and tilted it up, Apoc's fingers brushed gently around his eyes. His friend muttered to himself quietly, "Oh God. How ? How could that happen ?"

Confused and definitely frightened, he asked, "W-what ? H-how could what happen, Ap-Apoc ?"

It was odd hearing Apoc's concerned tone and not being able to see it. "The-the glass, somehow it's-it's melted over your eyes. How could it be that hot ? I-I don't get this. This isn't natural, I-I'll try to clean you up a bit. Can you see anything ?"

His friend moved to help him get up and he replied, "The metal I can see that, I think the light's dull gold since it's cold. I see that, but I can't see you. Apoc, to me, you might as well not exist. I could be talking to myself and I wouldn't be able to tell, you're just a black spot, a-a nothing. Oh God, Apoc, I'm **blind** !"

_'How am I supposed to get into the Machine City if all the metal looks the same ? How will I even be sure I won't walk off a cliff or into a chasm ? Thank God for Apoc or I'd be doomed now.'_


	12. Chapter 11 - Machines

**Machines**

Neo ran a hand over the 'bandage' that Apoc had tied around his eyes a few minutes ago, while he'd told Apoc about his EMP/energy manipulation. Despite the bandage, he could still see the metal and as he walked into the Logos' Core, he saw Niobe's jack-in chair, but not the woman herself.

_'What's so different from humans to metal ? What the hell is that ?'_

As soon as he'd gotten maybe two feet away, the chair had changed from a shade of light orangeto a much deeper one. Intrigued, he walked over to put a hand on it as he did, the chair emitted a strange sound as energy thrummed from the human fields below. Somehow, he found himself listening to the Matrix through Niobe's ears.

Felt Smith looking down at him/Niobe as the ex-Agent growled, "Why didn't he believe me ?"

"Maybe, just, maybe, it's because you've taken to **lying** to him. Plus, the fact that you've turned into a gigantic asshole, despite, claiming that you love him."

Felt the pressure as Smith picked him/Niobe up by the throat and threw 'them'. Heard the impact as 'they' smacked into a tree.

Listened as Smith's emotional switch flipped from anger a second later into regret, "Yes, I lied to him about Bane at first, it was only because I wanted him to be happy without knowing the difference between the real Bane and myself."

He was back in his own body as Apoc's voice came over the intercom, "Neo, you're gonna want to get up here. We've got a fuck-load of Squiddies inbound."

Quickly, he let go of the chair and started out of the Core, as Apoc audibly guided him to the Logos' cockpit. While he walked in thoughts spun in his head, _'I'm going to have to do a lot of work with a tiny bit of energy. This is when it sucks that we've gotta rescue Niobe from Smith, we can't use the regular EMP without killing her. We're gonna die, we're so going to die. No, no we've gotta live till we save Niobe and Zion, at least. After that, it won't matter anymore. Holy shit that __**is **__a fuck-load of Squiddies.'_

There were so many Sentinels flying toward them he couldn't see the towers' energy for Sentinels'. _'There has to be over a hundred of 'em. Fuck.' _Shook his terror away as he sat beside Apoc and drew some of the towers' energy to himself before he threw it into the front lines.

The first Sentinels the energy wave hit fell to the ground fried, the second wave stopped in mid-air frozen. At least, until the Logos' smashed into them and they started slamming claw-tentacles into the windshield. This time he took the energy from the ones attacking the windshield as the Logos was jarred from behind.

There was some sort of alarm before Apoc said, "We just lost a hover-pad, Neo."

"Don't tell me that !"

Every time he pulled energy from either the towers or the Squiddies, to save the Logos from most damage, it took more and more out of his already tired body. Still, it felt to him that the main energy was getting stronger. _'We've gotta be close to the Machine City now, we have to be. God, hold on Niobe, we're so close to you.'_

The Squiddies fell away from in front of them and he spotted three really bright-gold lines in the ground. "There Apoc do you see it ? That trio of lines, they've got to be the towers power source."

One of the only reasons he knew Apoc would be nodding was experience. Apoc replied, as he felt the Logos move toward the lines, "Good, cause we can't take much more punishment. I don't like this, why'd they suddenly stop coming ?"

He nodded, "Something's got to be up."

Time seemed to drag if only because of the nervous silence that'd fallen over them. His heart rate seemed impossibly fast as it pounded in his ears. Nearly had a heart attack as something collided with the Logos. Even the golden 'light' disappeared as he was 'blinded' by the sound of an explosion before the Logos started to fall from the sky. Seconds later, he was thrown through the windshield as the hovercraft crashed. Scrabbled to try and push himself up, only to fall back to the ground. It was rocky and studded with metal shards.

Apoc's voice called, "Neo ? W-where are you ?"

"I'm over here, you ?"

"You'll have to follow my voice."

So, too weak to walk he crawled toward Apoc's voice and cut up his hands on the shards. Everything had drained him so much the pain didn't seem real. Just when he thought he'd never find Apoc, he accidentally put a hand on Apoc's chest.

The man exclaimed weakly, "Ow."

"Sorry, Apoc, I didn't mean to. Are you all right ? You sound even worse than I do."

A soft chuckle, "It won't matter too long."

_'What ? No, I refuse to believe what he's implying.'_

Shook his head and exclaimed, "Apoc, no, you're not making sense ! You've got to show me how to get to the Machine City. We've done nearly everything together, you've got to help end this. It's not right otherwise."

A hand touched his shoulder briefly, "I'm sorry, I know you'll do fine…little brother."

That made his breath catch from grateful shock, "Little** brother** ? You really think so ?"

_'Little brother ? He's never called me that before.'_

Again, there was no answer from the man who'd turned from his friend to his brother. Except, this time Apoc's silence was more ominous.

_'No. __**No**__. __**Not Apoc too.**__'_

His hand shook as he moved it to Apoc's neck. For a second he didn't want to, then he decided he had to do it. Slowly, he put his fingers on his friend's throat it felt like it was covered in blood. Let out a harsh sob as he realized that Apoc - the man who'd helped him through his first days and through the many taunts from Cypher, who'd defended him from homophobic idiots, the man who'd always been there for him no matter what - was dead.

Even if he'd been able to, his body was too exhausted to cry or even really sob. Too tired to move, he just wanted to lie there and screamed, "**God-fucking-damn it, why **? I just want it to be over. I'm tired of people dying I just want some peace. Peace, is that so hard ?"

_'I can't stay here, Apoc wants me to finish it. It'll hurt even more, but this is the last straw. Tonight, today, whatever time it is…this is the beginning of the end…even if it's my end.'_

Pried himself away from Apoc's body and forced himself to stagger up right. Forced himself to walk, when he fell he rested for a second, then body screaming in agony he crawled until he could walk again. All the while instinct pulled him toward a gigantic energy source - the Machine City.

Distantly, he saw Sentinels' start to approach him, then they stopped before they hovered along a path. If he stopped, the Sentinels would stop, as if they wanted him to follow them. Eventually, the Sentinels led him to the edge of a precipice and a whole bunch of little Machines of a type he'd never seen before flew up and around until they formed a giant circle in front of him.

A single voice came from the circle, "We know of you, One, why do you come here ?"

_'I can't believe I'm actually here. It's almost over and they know it. Do they want it to end ? If they don't my words won't matter, Niobe and Zion will be gone. Bane, Ballard, Soren and Apoc will have died for nothing. Please, let this work.'_

Barely able to keep his eyes open, he forced the words out, "My friends are living, dying or dead and the Matrix is practically gone. Who knows how many of your Machines have been deleted. This all because of me and Smith. I'm tired of all this fighting, so, since you've been at this longer than I have I figure that you must be tired of wasting resources to fight, then destroy and re-build Zion all the time. I just want some peace and Smith's in the way of that peace, he wants to destroy everything, even you. Surely, you know that."

The giant Machine replied, "The Matrix is almost out of our control, we know we can not stop him. What makes you think you can stop him ? When all our Agents couldn't ? Even as the One, you would have a very hard time of reaching him alone, much less fighting him. Do you think peace is worth risking all of our existences ?"

Bowed his head before he said, "Smith might be insane, but he still somewhat loves me. That means he'll, probably, let his guard down and if it comes to a fight, I can use that against him. I've got to try for all of our sakes human and Machine, or else none of this will have mattered."

Didn't expect the Machine to agree with him and say, "Good, if you stop him, we will have peace. Now, we will give you something to write this down for future reference. When you have finished we will plug you into the Matrix."

…

That is how I came to write this letter to you, whether you will need to read it or be able to I don't know.

Wish me luck,

Neo


	13. Chapter 12 - Smith

**Smith**

Neo felt the jack slide into his neck and then silence turned into the sound of wind rustling through trees. It gave him a bit of energy back, that made him try to open his eyes. Despite being amazed when he could…_'This is disappointing. I'd hoped to see again in here, apparently, nope. Damn it, aw crap.'_

Slowly, he'd taken a step, fallen and rolled down a hill to slam into a tree. Groaned as he used the tree trunk to help himself up. _'Nice to see the Machines care about my welfare. I should be dead after getting the shit hit or kicked out of me every five minutes. I hope Niobe's been having a less painful time. Where are they ? Did I get sent to the wrong spot ?'_

Hesitantly, he called, "Smith ? Niobe ? Anybody ?"

Branches snapped as somebody started walking towards him. Smith answered, in such a concerned tone it was painful to hear, "Neo ?"

_'Smith's here, so, Niobe's got to be here somewhere.'_

He stumbled and flailed as he tried to find a way around the tangled tree roots without falling. This time he didn't fall if only because Smith's arms wrapped around him. After all the pain, even if it wouldn't last, it felt good to lean into the solid warmth. _'Even after all this, I could still stay here forever.'_

As the wind rustled again, he asked, "Smith, where are we ?"

Shivered and felt a bit uncomfortable as Smith slid a hand over the back of his neck and started to play with his hair. "The forest where I told you about Bane. Why do you ask and why won't you look at me ?"

_'If he's going to get mad over anything it'll be this.'_

For a second he bit his lip, before he said. "Jones copied over Lupa, then he got on the Logos with Apoc and I. He trapped Apoc, before he knocked me out. After I woke up, me and Apoc we got free, after a bit of a fight, well, Jones smashed a light into my face, so, it's not like I don't want to. It's because I can't…I'm blind now."

A growled, "I'll delete that fuck again, I'll make sure he can never touch you."

Niobe yelled from probably ten feet away, "Maybe Neo doesn't want you touching him either, Smith."

The brown-haired A.I. let go of him before he heard Smith turn and snarl, "I have finally had enough of your attitude, Miss. Morris."

He put a hand on Smith's arm and shook his head, "Why did you kidnap Niobe ? What did you want with her ?"

_'Answer me, damn it. __**Answer**__ me.'_

Smith ignored his question, before roughly shaking off his hand, and stalked toward Niobe. Couldn't suppress the shudder at the sound of the Desert Eagle being fired. It brought back the dim memories of Jones's bullets killing him. That made him exclaim as he rushed to get in between the two, "**Niobe** ? ! Smith ! What in Balroanian hell do you think you're doing ? She's my friend."

"Do you know how incredibly **frustrating** it was ? Watching her slip away time and time again over the years ? Every time she would just barely manage to get away. Considering that she's already turned you against me, I refuse to let her go, not when I can finally end her."

"Why ? Smith, why would you wait for me then if you really wanted to kill her ? Apoc's dead, Switch and Niobe are the only best friends I have left. I can't let you kill her and unless you want to kill me too, you won't."

"If you refuse to move then I guess I will have to, love."

Shook his head and demanded, "Stop calling me that then. If you're going to kill me, you're not the Smith I know. The one that I fell in love with and came back for."

Before he could think, he ducked as a punch flew over his head. He grabbed the Desert Eagle with one hand and twisted it away from Smith before he focused and threw it, then slammed a open-palm into Smith's chest. A barely audible grunt before a heavy punch impacted with his injured shoulder.

The hit sent him flying into another tree which shook from it. He gasped as a kick connected with his ribs. In reality, he didn't even recover from that before he was being choked. If his desperation fuelled kicks connected with Smith, the ex-Agent refused to react to them. That desperation turned to clawing at the tanned-hands that were firmly locked around his throat. If his vision hadn't already been black, it would have started disappearing.

_'So, just like how Jones tried to kill me in the wall. Ironic that now Smith's the one doing it and no one's here to save me from him.'_

One hand loosened to mockingly caress his throat, then Smith laughed and he felt the tree shake, again, "It should please you to know that the **real** Smith is screaming at the top of his lungs for me to stop. Not that it will change anything now, but he actually does love you, you know."

_'Real ? What the fuck does that even mean anymore ?'_

Niobe exclaimed, "Koro, get the fuck out of him ! Or I'll kill you."

Smith or, uh, Koro growled, "Really, Niobia ? After all we went through ? You could have stopped this, if you'd told him, but you didn't. Even for our kind you're a goodie two-shoes. Now, Neo, you wanted to know what a Balroanian is ? I'll be generous and let you see for a few seconds."

In an instant his vision was back and he stared in shock - it wasn't Smith pining and choking him now. Smith didn't have long light-blond hair, a bright-green eye and a dark-gray eye and definitely didn't have a pair of dark-gray furred, bat-like wings. Koro grinned showing four sharp, wolf-like canines.

Koro hummed, the wings shifted and rustled, "I should have been cut-off a long time ago, I never liked your insipid kind and everyone knew it."

Niobe/Niobia growled, "Well, now you can die."

Just before a black knife emerged from Koro's chest. Then it was Smith let go of him and backed into Niobe, looking horrified. Niobe's dark-red furred wings flared open as Smith dropped to his knees on the ground. It was the last thing he saw before his vision went black again.

The ex-Agent cried, "I'm sorry ! I am so sorry, my love. This is all my fault, I could not resist him."

He coughed and rubbed his throat as he slumped against the tree. "It's not your fault, Smith. That Koro or whatever his name was, was controlling you. There's nothing you could've done."

"No, Neo. You do not understand, before I met you, I would have given nearly anything to kill her. Yes, he might have wanted to kill her before, but it was still my fault. I would have killed you just barely because of him."

Twigs snapped as Smith got up and ran. _'Where's he going ?_ _What does this mean ? Was Jones possessed too or was he just that crazy ?'_

Niobe's voice as the woman/Balroanian walked up to him, "He'll get slightly better, eventually. No, Jones wasn't possessed by one of my kind, he was just that jealous of Smith. For that matter, I'm just me, I was sent to help out and I ended up finding very good friends."

"Niobe, do you know what happened to Apoc and the others ?"

"They're safe, don't you worry about that. I'll send you back and you can tell Deus that Smith won't try to take over anything ever again."

In response he nodded and then everything turned to silence.

* * *

><p><strong><span>Epilogue …<span>**

Neo startled as Switch draped an arm around his shoulders. '_God, it's been a year and I, we, both still miss Apoc. Even though we know he's okay, I guess that's what happens when you can't see someone for yourself.'_

The pale-skinned blond woman muttered as she knocked on Smith's door, "Nice of you to get Smith to invite us, little brother. Too bad you can't see the new house, it's two storeys, got white paint and gray shingles, hell, there's even a 'Welcome' mat. You ask me, Smith's getting possessed is the second best thing to happen to him."

He laughed and shook his head, "He's definitely a lot friendlier now. Niobe's not going to make it today ?"

"Not that I know of, it's a real shame since he's feeding us too. Did you know he could cook ?"

That made him wonder if Niobe was off visiting Apoc, Soren and Ballard. Or if the Logos Captain was back in Zion with Ghost and Sparks.

Shook himself before he replied, "Uh, I didn't really."

The door to Smith's house opened and a hand took his, before he was gently pulled inside to sit down on the couch. Shivered as the ex-Agent greeted warmly, "Hello, Neo, hello, Switch."

Switch chuckled as she sat beside them on the couch. The door closed itself and Smith asked, "What does everyone want to watch ?"

Both Switch and himself chorused, "Doesn't matter."

Smith replied, "Well, I found something interesting at the store today. It's a little movie called The Matrix."

He raised an eyebrow, "They actually made a movie about all of us ?"

"Yes and apparently it's a very good movie. Shall I describe how well they cast us for you ? The resemblance to us and our friends is simply uncanny."

_'It's taken me months to get over the fact it wasn't him that snapped at and hit me. At least, now I actually feel comfortable around him again. Maybe we can get back to our romance, eventually.'_

Unconsciously, he leaned into Smith as he nodded.

* * *

><p><span><em>Ending <em>_Author's__ Note:_Thanks for reading everybody and thanks to_ blackcat21223 _for the favourite.


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